rs2272306

chr12-53160499-G-Achr12-53160499-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001244705.2(CSAD):c.967-180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,170 control chromosomes in the GnomAD database, including 1,059 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1059 hom., cov: 32)
• Consequence: CSAD NM_001244705.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

Genes affected

CSAD (HGNC:18966): (cysteine sulfinic acid decarboxylase) This gene encodes a member of the group 2 decarboxylase family. A similar protein in rodents plays a role in multiple biological processes as the rate-limiting enzyme in taurine biosynthesis, catalyzing the decarboxylation of cysteinesulfinate to hypotaurine. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSAD	NM_001244705.2	c.967-180C>T		intron_variant		ENST00000444623.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSAD	ENST00000444623.6	c.967-180C>T		intron_variant		1	NM_001244705.2	P1
	ENST00000550908.1	n.401+219G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16235 AN: 152052 Hom.: 1059 Cov.: 32

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.116

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.107 AC: 16237 AN: 152170 Hom.: 1059 Cov.: 32 AF XY: 0.108 AC XY: 7999 AN XY: 74396

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0957

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.115

Alfa AF: 0.126 Hom.: 1742

Bravo AF: 0.106

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.4
Dann	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2272306; hg19: chr12-53554283;